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Background: Breast cancer ranks as the second highest cause of cancer-linked deaths in women, with varying rates between Western and Asian countries. The consumption of phytoestrogens can influence breast cancer occurrence., Objective: To comprehend how soy isoflavones impact breast cancer cells, we conducted a meta-analysis, combining gene expression data from multiple studies. This approach aimed to identify crucial transcriptional characteristics driving breast cancer cell response to soy phytoestrogens., Materials and Methods: The gene expression profiles obtained from the Gene Expression Omnibus and Array Express and were grouped into control and isoflavones exposure conditions. We performed a meta-analysis based on the effect size combination method to identify the differentially expressed genes (DEGs). In addition, we performed Gene Ontology (GO) enrichment analysis, pathway analysis, weighted gene co-expression network analysis (WGCNA) and recursive support vector machine (R-SVM) algorithm., Results: Based on this meta-analysis, we identified 3,890 DEGs, of which 2,173 were up-regulated and 1,717 were down-regulated. For example, SGCG , PLK2 , and TBC1D9 were the most highly down-regulated genes and EGR3 , WISP2 , and FKBP4 were the most highly expressed genes in the isoflavones exposure condition. The functional enrichment and pathway analysis were revealed "cell division" and "cell cycle" among the most enriched terms. Among the identified DEGs, 269 transcription factor (TF) genes belonged to 42 TF families, where the C 2 H 2 ZF, bZIP, and bHLH were the most prominent families. We also employed the R-SVM for detecting the most important genes to classify samples into isoflavones exposure and control conditions. It identified a subset of 100 DEGs related to regulation of cell growth, response to estradiol, and intermediate ribonucleoside monophosphate in the purine (IMP) metabolic process. Moreover, the WGCNA separated the DEGs into five discrete modules strongly enriched for genes involved in cell division, DNA replication, embryonic digit morphogenesis, and cell-cell adhesion., Conclusion: Our analysis provides evidence suggesting that isoflavone affects various mechanisms in cells, including pathways associated with NF-κB, Akt, MAPK, Wnt, Notch, p53, and AR pathways, which can lead to the induction of apoptosis, the alteration of the cell cycle, the inhibition of angiogenesis, and interference in the redox state of cells. These findings can shed light on the molecular mechanisms that underlie the response of breast cancer cells to isoflavones., Competing Interests: The authors declare no competing interests., (Copyright: © 2021 The Author(s); Published by Iranian Journal of Biotechnology.)

Background: When Salmonella enterica serovar Typhimurium , a foodborne bacterium, is exposed to osmotic stress, cellular adaptations increase virulence severity and cellular survival., Objectives: The aim of the gene network analysis of S. Typhimurium was to provide insights into the various interactions between the genes involved in cellular survival under low water activity (a w )., Materials and Methods: We performed a gene network analysis to identify the gene clusters and hub genes of S. Typhimurium using Cytoscape in three food samples subjected to a w stress after 72 hours., Results: The identified hub genes of S. Typhimurium belonged to down-regulated genes and were related to translation, transcription, and ribosome structure in the food samples. The rpsB and Tig were identified as the most important of the hub genes. Enrichment analysis of the hub genes also revealed the importance of translation and cellular protein metabolic processes. Moreover, the biological process associated with organonitrogen metabolism in milk chocolate was identified. According to the KEGG pathway results of gene cluster analysis, cellular responses to stress were associated with RNA polymerase, ribosome, and oxidative phosphorylation. Genes encoding RNA polymerase activity, including rpoA , rpoB , and rpoZ , were also significantly identified in the KEGG pathways. The identified motifs of hub DEGs included EXPREG_00000850, EXPREG_00000b00, EXPREG_000008e0, and EXPREG_00000850., Conclusion: Based on the results of the gene network analysis, the identified hub genes may contribute to adaptation to food compositions and be responsible for the development of low water stress tolerance in Salmonella . Among the food samples, the milk chocolate matrix leads to more adaptation pathways for S. Typhimurium survival, as more hub genes were down-regulated and more motifs were detected. The identified motifs were involved in carbohydrate metabolism, carbohydrate transport, electron transfer, and oxygen transfer., (Copyright: © 2021 The Author(s); Published by Iranian Journal of Biotechnology.)

Acorn is a nutritious fruit with the reported potential of ameliorating diseases, including diabetes. This research aimed to assess the effects of acorn muffin consumption on glycemic, lipid indices, and appetite in patients with type 2 diabetes. Sixty-six subjects were dichotomized to receive either one muffin containing 10 grams of acorn flour or a placebo muffin containing white wheat flour (no bran), per day, for 8 weeks. Acorn muffin consumption improved glycated hemoglobin ( p  = .06, mean difference [MD] = -0.65), triglyceride ( p  = .06, MD = -36.38), and high-density lipoprotein ( p  = .05, MD = 1.30), albeit only marginally significantly. Among appetite parameters, hunger, desire to eat, and prospective to eat were significantly lower, and satiety and fullness were significantly higher, in the acorn muffin group. In conclusion, acorn muffins could be utilized as an adjuvant therapy to control appetite and ameliorate glycated hemoglobin in patients with type 2 diabetes. However, further investigations are required for a more comprehensive conclusion., Competing Interests: None., (© 2022 The Authors. Food Science & Nutrition published by Wiley Periodicals LLC.)

Systemic arterial hypertension is an independent risk factor for coronary heart disease, stroke, heart failure, and chronic kidney diseases. Spirulina is microalgae with nutritious ingredients and has potential attenuating effects on chronic diseases including hypertension. Spirulina can be added to food products in order to develop functional foods. The aim of this study was to assess the effects of 8-week consumption of a salad dressing containing 2 g of spirulina platensis powder versus a placebo dressing on patients with hypertension. In this triple-blind randomized clinical trial, 48 patients with hypertension were enrolled to receive daily either spirulina-fortified dressing or placebo for 2 months. A total of 41 patients completed this study. We observed that the consumption of spirulina dressing significantly reduced systolic blood pressure (p = .02), diastolic blood pressure (p = .03), serum triglyceride (p = .01), total cholesterol, and low-density lipoprotein (LDL) levels, compared to nonsignificant changes in the placebo group. Significant changes in TAC and hs-CRP levels were observed in none of the groups. According to our findings, spirulina-fortified dressing as a functional food can be used a supportive treatment for patients with hypertension along with standard antihypertensive drugs. However, further investigations are required for a more comprehensive conclusion., (© 2021 John Wiley & Sons Ltd.)

Abiotic environmental stresses are important factors that limit the growth, fiber yield, and quality of cotton. In this study, an integrative meta-analysis and a system-biology analysis were performed to explore the underlying transcriptomic mechanisms that are critical for response to stresses. From the meta-analysis, it was observed that a total of 1465 differentially expressed genes (DEGs) between normal and stress conditions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that DEGs were significantly enriched in the ubiquitin-dependent process, biosynthesis of secondary metabolites, plant hormone, and signaled transduction. The results also indicated that some of DEGs were assigned to transcription factors (TFs). A total of 148 TFs belonged to 25 conserved families were identified that among them S1Fa-like, ERF, NAC, bZIP families, were the most abundant groups. Moreover, we searched in upstream regions of DEGs for over-represented DNA motifs and were able to identify 11 conserved sequence motifs. The functional analysis of these motifs revealed that they were involved in regulation of transcription, DNA replication, cytoskeleton organization, and translation. Weighted gene co-expression network analysis (WGCNA) uncovered 12 distinct co-expression modules. Four modules were significantly associated with genes involved in response to stress and cell wall organization. The network analysis also identified hub genes such as RTNLB5 and PRA1, which may be involved in regulating stress response. The findings could help to understand the mechanisms of response to abiotic stress and introduce candidate genes that may be beneficial to cotton plant breeding programs., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

A wide range of biotic stresses (BS) and abiotic stresses (AS) adversely affect plant growth and productivity worldwide. The study of individual genes cannot be considered as an effective approach for the understanding of tolerance mechanisms, since these stresses are frequent and often in combination with each other, and a large number of genes are involved in these mechanisms. The availability of high-throughput genomic data has enabled the discovery of the role of transcription factors (TFs) in regulatory networks. A meta-analysis of BS and AS responses was performed by analyzing a total of 391 microarray samples from 23 different experiments and 2,336 differentially expressed genes (DEGs) involved in multiple stresses were identified. We identified 1,862 genes differentially regulated in response to BS was much greater than that regulated by AS, 835 genes, and found 15.4% or 361 DEGs with the conserved expression between AS and BS. The greatest percent of genes related to the cellular process (>76% genes), metabolic process (>76% genes) and response to stimulus (>50%). About 4.2% of genes involved in BS and AS responses belonged to the TF families. We identified several genes, which encode TFs that play an important role in AS and BS responses. These proteins included Jasmonate Ethylene Response Factor 1 (JERF1), SlGRAS6, MYB48, SlERF4, EIL2, protein LATE ELONGATED HYPOCOTYL (LHY), SlERF1, WRKY 26, basic leucine zipper TF, inducer of CBF expression 1-like, pti6, EIL3 and WRKY 11. Six of these proteins, JERF1, MYB48, protein LHY, EIL3, EIL2 and SlGRAS6, play central roles in these mechanisms. This research promoted a new approach to clarify the expression profiles of various genes under different conditions in plants, detected common genes from differentially regulated in response to these conditions and introduced them as candidate genes for improving plant tolerance through genetic engineering approach., Competing Interests: The authors declare that they have no competing interests.